Epithelial ovarian cancer, the most prevalent form of ovarian cancer, is a health concern worldwide. Phosphoserine aminotransferase 1 (PSAT1), as the rate‑limiting enzyme in serine synthesis, is key in the conversion of 3‑phosphoglycerate to serine. The present study explored the role of PSAT1 expression in epithelial ovarian tumors. Gene Expression Profiling Interactive Analysis was used for gene expression and survival analyses. The effects of PSAT1 overexpression and knockdown on invasion, migration, proliferation and cell cycle progression of ovarian cancer cell lines were investigated both in vitro and in vivo. Western blotting was conducted to assess alterations in PI3K/AKT signalling pathway proteins. Database and tissue sample data confirmed that PSAT1 was significantly upregulated in ovarian cancer. Preliminary functional investigations indicated that PSAT1 was involved in modulation of invasion and migration, demonstrating the capacity of PSAT1 to enhance expression of the PI3K/AKT signalling pathway. These findings suggested that PSAT1 served a critical role in the onset and progression of ovarian cancer, thereby offering a theoretical basis for early detection and therapeutic strategies.

N6-methyladenosine (m6A) modification is an important mechanism in microRNA processing and maturation. Previous studies show the involvement of pri-miRNA methylation in regulating the occurrence and development of tumor-related diseases. In this study, we investigated the role of its aberrant regulation in cardiac diseases. Myocardial infarction (MI) mouse were established by ligation of the left anterior descending branch of the coronary artery. We showed that the expression of methyltransferase 14 (METTL14) was significantly increased in myocardium of MI mice. We demonstrated that METTL14 methylated the primary transcript miRNA (pri-miR-5099), promoting the recognition by DiGeorge critical region 8 (DGCR8) and the maturation processing of pri-miR-5099. Mature microRNA-5099-3p (miR-5099-3p) inhibited the expression of E74 like ETS transcription factor 1 (ELF1), which transcriptionally regulated pyroptosis factors such as acysteinyl aspartate-specific proteinase 1 (caspase-1) and gasdermin D (GSDMD), ultimately leading to cardiomyocyte pyroptosis. This study reveals that myocardial infarction-induced miR-5099-3p excessive maturation via m6A modification promotes the development and progression of cardiomyocyte pyroptosis.

Triple-negative breast cancer (TNBC) is characterized by the absence of targeted therapies and a dismal prognosis, necessitating a critical exploration of the molecular mechanisms driving TNBC pathogenesis and the identification of novel therapeutic targets. While dysregulated USP5 expression has been observed in various malignancies, its specific functions and mechanisms in TNBC remain poorly understood.

The study utilized a combination of TCGA database analysis, immunohistochemistry staining (IHC), quantitative RT-PCR, and western blotting assay to investigate the expression of USP5 and SP1 in TNBC. Furthermore, the study examined the role of the SP1-USP5 axis and the USP5 inhibitor periplocin in TNBC progression through CCK-8 assay, colony formation assay, EDU incorporation assay, and tumor xenograft experiments. Additionally, the study explored the underlying mechanisms involved in the regulation of USP5 expression in TNBC using luciferase assay, ChIP-qPCR, quantitative RT-PCR, and western blotting assay. In order to ascertain potential inhibitors of USP5 activity, a combination of the Molecular Operating Environment (MOE) multi-functional docking platform, cellular thermal shift assay, and in vitro USP5 activity assay were utilized.

In the current investigation, it was observed that the expression of USP5 was elevated in TNBC and was significantly correlated with decreased overall survival rates among patients. The upregulation of USP5 was found to be mediated by the transcription factor SP1 through its binding to the USP5 promoter, consequently facilitating the progression of TNBC. Notably, the natural compound periplocin was identified as a promising inhibitor of USP5, demonstrating potential efficacy in impeding the advancement of TNBC.

Our research findings indicate that the SP1-USP5 signaling pathway is significantly involved in the advancement of TNBC, and periplocin's ability to target USP5 presents a potential therapeutic approach for managing TNBC. These results offer valuable insights for the development of novel treatment strategies for TNBC patients.

The ABCB1 gene, encoding the ATP-dependent translocase ABCB1, plays a crucial role in the clearance of amyloid-beta (Aβ) peptides and the transport of cholesterol, implicating it in the pathogenesis of Alzheimer's disease. The study aims to investigate the association between polymorphisms in the ABCB1 gene and cognitive decline in individuals with mild cognitive impairment (MCI), particularly focusing on language function. A longitudinal cohort study involving 1 005 participants from the Czech Brain Aging Study was conducted. Participants included individuals with Alzheimer's disease, amnestic MCI, non-amnestic MCI, subjective cognitive decline, and healthy controls. Next-generation sequencing was utilized to analyze the entire ABCB1 gene. Cognitive performance was assessed using a comprehensive battery of neuropsychological tests, including the Boston Naming Test and the semantic verbal fluency test. Ten ABCB1 polymorphisms (rs55912869, rs56243536, rs10225473, rs10274587, rs2235040, rs12720067, rs12334183, rs10260862, rs201620488, and rs28718458) were significantly associated with cognitive performance, particularly in language decline among amnestic MCI patients. In silico analyses revealed that some of these polymorphisms may affect the binding sites for transcription factors (HNF-3alpha, C/EBPβ, GR-alpha) and the generation of novel exonic splicing enhancers. Additionally, polymorphism rs55912869 was identified as a potential binding site for the microRNA hsa-mir-3163. Our findings highlight the significant role of ABCB1 polymorphisms in cognitive decline, particularly in language function, among individuals with amnestic MCI. These polymorphisms may influence gene expression and function through interactions with miRNAs, transcription factors, and alternative splicing mechanisms.

Vascular smooth muscle cells undergo a phenotypic shift to a "synthetic" phenotype during atherosclerosis characterized by downregulation of contractile markers and augmented proliferation, migration, and extracellular matrix deposition. While absent in contractile smooth muscle cells, the receptor tyrosine kinase EphA2 shows enhanced expression in synthetic vascular smooth muscle in vitro and in atherosclerotic plaques in vivo. EphA2 deletion in atheroprone ApoE knockout mice reduces plaque size, fibrous tissue, and smooth muscle content. However, the mechanisms regulating smooth muscle EphA2 expression remain unknown. Although serum strongly induces EphA2 expression, individual growth factors and insulin all failed to stimulate EphA2 expression in smooth muscle cells. In contrast, adhesion to fibronectin stimulated the expression of EphA2, while blunting serum-induced fibronectin deposition attenuated EphA2 expression, suggesting a critical role for fibronectin signaling. Fibronectin binds to a subset of extracellular matrix-binding integrins, and blocking fibronectin-integrin interactions or inhibiting specific fibronectin-binding integrins both attenuated EphA2 expression. Furthermore, pharmacological inhibition of fibronectin-binding integrins significantly reduced EphA2 expression in atherosclerotic plaques. RNA sequencing analysis of fibronectin-associated gene expression pointed to NF-κB as a likely transcription factor mediating fibronectin-responsive genes. Adhesion to fibronectin enhanced NF-κB activation in smooth muscle cells and inhibiting NF-κB blunted EphA2 expression associated with fibronectin. In addition, chromatin immunoprecipitation showed that NF-κB directly interacts with the EphA2 promoter, and mutating this site blunts fibronectin-dependent EphA2 promoter activity. Together these data identify a novel role for fibronectin-dependent integrin signaling in the induction of smooth muscle EphA2 expression.NEW & NOTEWORTHY Here, we demonstrate a novel interplay between cell-cell and cell-matrix adhesions, showing that fibronectin-dependent integrin signaling promotes NF-κB activation and interaction with the EphA2 promoter to drive smooth muscle EphA2 expression, whereas integrin inhibition attenuates EphA2 expression in atherosclerotic plaques in vivo. Although this relationship has clear implications on smooth muscle fibroproliferative remodeling in atherosclerosis, the matrix-specific regulation of EphA2 expression may impact a variety of pathological conditions.

The SWEET (Sugar Will Eventually be Exported Transporters) protein family plays a key role in plant growth, adaptation, and stress responses by facilitating soluble sugar transport. However, their functions in Cymbidium remain poorly understood. This study identified 59 SWEET genes across four Cymbidium species, encoding conserved MtN3/saliva domains. Despite variations in exon-intron structures, gene motifs and domains were highly conserved. Phylogenetic analysis grouped 95 SWEET proteins from six species into four clades, with gene expansion driven by whole-genome, segmental, and tandem duplications. Cis-element analysis and expression profiling across 72 samples revealed diverse regulatory patterns. Notably, SWEET genes showed peak expression in floral development, leaf morph variations, and diurnal rhythms. qRT-PCR and transcription factor binding analysis further highlighted their regulatory roles in floral patterning, leaf variation, and metabolic rhythms. These findings provide a foundation for future studies on SWEET gene function and their potential molecular breeding value in orchids.

Recent advancements in animal genetics, biotechnology, and bioinformatics can potentially contribute to the required improvement in fish production and quality. Current study explored for the first-time, various genes from Transforming growth factor-beta (TGF-β) gene family which could play vital role in growth and development of Labeo rohita, an economically important freshwater fish. A number of tools and analysis like characterizing the selected genes, multiple alignment and clade-wise phylogeny, dual Synteny analysis and chromosomal distribution, characterization of proteins, secondary structure and 3D models of proteins, PROSITE scan analysis, and transcription factor binding sites (TFBSs) of selected genes were performed to explore the relationship between selected genes from Labeo rohita and referenced species (Homo sapiens, Danio rerio, Oreochromis niloticus, Chelonia mydas, and Parus major). The study evaluated 27 genes from TGF-β gene family. The results suggested that physicochemical characteristics of studied genes exhibit a basic nature with the few exceptions. Two main clades (BPM like and GDF like) were obtained by the phylogenetic analysis across six vertebrate species. Homogeneity was observed in the gene structure for all selected genes of TGF-β gene superfamily. TGF-β family and TGF-β propeptide family were dominant in domain regions of studied genes. Gene structure comparisons suggested that the TGF-β gene superfamily has arisen by gene duplications events. The study identified five pairs of duplicated gene (segmental duplications) with the Ka/Ks < 1, indicating the negative selection pressure of these genes. The length of selected TFBSs (GATA, HOXD, STAT, HNF-1A, and YY1) ranged from 5 to 9 bp, with the HOXD having maximum bp. This study explored the molecular characterization for TGF-β gene family and related proteins in L. rohita and will potentially serve as basis of development of novel strategies in improvement of fish culture.

The canonical functions of vimentin in cell mechanics and migration have been recently expanded by the discovery of new roles for extracellular vimentin (ECV) in immune responses to infection, injury and cancer. In contrast with the predominantly filamentous form of intracellular vimentin, ECV exists largely as soluble oligomers. The release of ECV from intact cells is dependent on mechanisms that regulate the assembly and disassembly of intracellular vimentin, which are influenced by discrete post-translational modifications. In this review we highlight the processes that promote the conversion of intracellular and insoluble vimentin filaments to ECV and secretion mechanisms. Insights into the regulation of ECV release from stromal and immune cells could provide new diagnostic and therapeutic approaches for assessing and controlling inflammatory diseases.

MicroRNAs (miRNAs) are small non-coding RNAs that play crucial roles in post-transcriptional gene regulation. Poly(A) RNA polymerase D5 (PAPD5) catalyzes the addition of adenosine to the 3' end of miRNAs. In this study, we demonstrate that the Yin Yang 1 protein, a transcriptional repressor of PAPD5, is recruited to both RNA foci and protein aggregates, resulting in an upregulation of PAPD5 expression in Huntington's disease (HD). Additionally, we identify a subset of PAPD5-regulated miRNAs with increased adenylation and reduced expression in our disease model. We focus on miR-7-5p and find that its reduction causes the activation of the TAB2-mediated TAK1-MKK4-JNK pro-apoptotic pathway. This pathway is also activated in induced pluripotent stem cell-derived striatal neurons and post-mortem striatal tissues isolated from HD patients. In addition, we discover that a small molecule PAPD5 inhibitor, BCH001, can mitigate cell death and neurodegeneration in our disease models. This study highlights the importance of PAPD5-mediated miRNA dysfunction in HD pathogenesis and suggests a potential therapeutic direction for the disease.

Hairy cell leukemia (HCL) is an indolent malignancy of mature B-lymphocytes. While existing front-line therapies achieve excellent initial results, a significant number of patients relapse and become increasingly treatment resistant. A major molecular driver of HCL is aberrant interlocking expression of the transcription factor JunD and the intracellular signaling molecule RhoH. Here we discuss the molecular basis of how the JunD-RhoH axis contributes to HCL pathogenesis. We also discuss how leveraging the JunD-RhoH axis identifies CD23, CD38, CD66a, CD115, CD269, integrin β7, and MET as new potential therapeutic targets. Critically, preclinical studies have already demonstrated that targeting CD38 with isatuximab effectively treats preexisiting HCL. Isatuximab and therapeutics directed against each of the other six new HCL targets are currently in clinical use to treat other disorders. Consequently, leveraging the JunD-RhoH axis has identified a battery of therapies that could be repurposed as new means of treating relapsed or refractory HCL.

Drought is a critical risk factor that impacts rice growth and yields. Previous studies have focused on the regulatory roles of individual transcription factors in response to drought stress. However, there is limited understanding of multi-factor stresses gene regulatory networks and their mechanisms of action. In this study, we utilised data from the JASPAR database to compile a comprehensive dataset of transcription factors and their binding sites in rice, Arabidopsis, and barley genomes. We employed the PyTorch framework for machine learning to develop a nine-layer convolutional deep neural network TFBind. Subsequently, we obtained rice RNA-seq and ATAC-seq data related to abiotic stress from the public database. Utilising integrative analysis of WGCNA and ATAC-seq, we effectively identified transcription factors associated with open chromatin regions in response to drought. Interestingly, only 81% of the transcription factors directly bound to the opened genes by testing with TFBind model. By this approach we identified 15 drought-responsive transcription factors corresponding to open chromatin regions of targets, which enriched in the terms related to protein transport, protein allocation, nitrogen compound transport. This approach provides a valuable tool for predicting TF-TAG-opened modules during biological processes.

Osteosarcoma (OS), a malignant bone tumor with limited treatment options, exhibits low sensitivity to immune checkpoint therapy (ICT). Through genomics and transcriptomics analyses, we identify a subgroup of OS with methylthioadenosine phosphorylase (MTAP) deletion, which contributes to ICT resistance, leading to a "cold" tumor microenvironment. MTAP-deleted OS relies on methionine metabolism and is sensitive to methionine intervention, achieved through either dietary restriction or inhibition of methionine adenosyltransferase 2a (MAT2A), a key enzyme in methionine metabolism. We further demonstrate that methionine intervention triggers programmed death-ligand 1 (PD-L1) transcription factor IKAROS family zinc finger 1 (IKZF1) and enhances PD-L1 expression in MTAP-deleted OS cells. Methionine intervention also activates the immune-related signaling pathways in MTAP-deleted OS cells and attracts CD8+ T cells, thereby enhancing the efficacy of ICT. Combining methionine intervention with ICT provides a significant survival benefit in MTAP-deleted OS murine models, suggesting a rationale for combination regimens in OS ICT.

The three-dimensional organization of the genome plays an important role in cellular function. Alterations between open and closed chromatin states contributes to DNA binding, collaborative transcriptional activities and informs post-transcriptional processing. The liver orchestrates systemic metabolic control and has the ability to mount a rapid adaptive response to environmental challenges. We interrogated the chromatin architecture in liver under different dietary cues. Using ATAC-seq, we mapped over 120,000 nucleosome peaks, revealing a remarkably preserved hepatic chromatin landscape across feeding conditions. Stringent analysis of nucleosome rearrangements in response to diet revealed that sex is the dominant factor segregating changes in chromatin accessibility. A lipid-rich diet led to a more accessible chromatin confirmation at promoter regions in female mice along with enrichment of promoter binding CCAAT-binding domain proteins. Male liver exhibited stronger binding for nutrient sensing nuclear receptors. Integrative analysis with gene expression corroborated a role for chromatin states in informing functional differences in metabolic traits. We distinguished the impact of gonadal sex and chromosomal sex as determinants of chromatin modulation by diet using the Four Core Genotypes mouse model. Our data provide mechanistic evidence underlying the regulation for the critical sex-dimorphic GWAS gene, Pnpla3 . In summary, we provide a comprehensive epigenetic resource in murine liver that uncovers the complexity of chromatin dynamics in response to diet and sex.

ATAC-Seq, RNA-Seq, and FCG model-integrated analysis unravel sex differences in chromatin accessibility and transcriptome responses to dietary challenges.Lipid-rich diet led to sex-biased chromatin confirmation at promoter regions.Gonadal sex emerged as the most prevalent determinant of the sex bias hepatic chromatin modulation by lipid-rich diets. The critical sex-dimorphic GWAS gene Pnpla3 is suppressed by testosterone, which underlies hepatic differences in expression between the sexes.

A recent pan-cancer transcriptome analysis indicated differential activity of alternative promoters of genes TNS3 and LRRFIP1 in head and neck squamous cell carcinoma compared to non-cancerous tissue. The promoters upregulated in head and neck squamous cell carcinoma regulate expression of transcripts TNS3-203 and LRRFIP1-211.

Our aim was to investigate the biomarker potential of TNS3-203 and LRRFIP1-211 transcripts in oral cancer, the most common type of head and neck cancer.

An in silico approach was used to characterize the promoters and transcripts of interest. Relative expression of TNS3-203 and LRRFIP1-211 transcripts was evaluated by qRT-PCR in a group of 46 oral cancer patients in samples of cancer and adjacent non-cancerous tissue.

TNS3-203 was significantly overexpressed in oral cancer compared with matched non-cancerous tissue, so this transcript can potentially be used as a diagnostic biomarker. There were no differences in LRRFIP1-211 level between analyzed tissues. None of the investigated transcripts has prognostic potential in oral cancer.

The results obtained indicate the diagnostic potential of TNS3-203, but not LRRFIP1-211 transcript and its role in oral carcinogenesis.

High fructose corn syrup (HFCS) is a commonly used sweetener in soft drinks and processed foods, and HFCS exacerbates inflammation when consumed in excess. Fructose, a primary component of HFCS; however, it is unclear whether fructose directly activates inflammatory signaling. Growth hormone secretagogue receptor (GHSR) is a receptor of the nutrient-sensing hormone ghrelin. We previously reported that GHSR ablation mitigates HFCS-induced inflammation in adipose tissue and liver, shifting macrophages toward an anti-inflammatory spectrum. Since inflammation is primarily governed by innate immune cells, such as macrophages in the peripheral tissues and microglia in the brain, this study aims to investigate whether GHSR autonomously regulates pro-inflammatory activation in macrophages and microglia upon fructose exposure. GHSR deletion mutants of RAW 264.7 macrophages and the immortalized microglial cell line (IMG) were generated using CRISPR-Cas9 gene editing. After treating the cells with equimolar concentrations of fructose or glucose for 24 h, fructose increased mRNA and protein expression of GHSR and pro-inflammatory cytokines (Il1β, Il6, and Tnfα) in both macrophages and microglia, suggesting that fructose activates Ghsr and induces inflammation directly in macrophages and microglia. Remarkably, GHSR deletion mutants (Ghsrmutant) of macrophages and microglia exhibited reduced inflammatory responses to fructose, indicating that GHSR mediates fructose-induced inflammation. Furthermore, we found that GHSR regulates fructose transport and fructose metabolism and mediates fructose-induced inflammatory activation through CREB-AKT-NF-κB and p38 MAPK signaling pathways. Our results underscore that fructose triggers inflammation, and reducing HFCS consumption would reduce disease risk. Moreover, these findings reveal for the first time that the nutrient-sensing receptor GHSR plays a crucial role in fructose-mediated inflammatory activation, suggesting that targeting GHSR may be a promising therapeutic approach to combat the immunotoxicity of foods that contain fructose.

Background: Breast cancer (BrCa) patients with tumors expressing high interleukin-6 (IL6) levels have poor clinical outcomes. In BrCa, altered occupancy of CCCTC-binding factor (CTCF) within its DNA binding sites deregulates the expression of its targeted genes. In this study, we investigated whether CTCF contributes to the altered IL6 expression in BrCa. Methods/Results: We performed CTCF gain- and loss-of-function assays in BrCa cell lines and observed an inverse correlation between CTCF and IL6 expression levels. To understand how CTCF negatively regulates IL6 gene expression, we performed luciferase gene reporter assays, site-directed mutagenesis assays, and chromatin immunoprecipitation assays. Our findings revealed that CTCF interacted with the IL6 promoter, a form of regulation disrupted in a CpG methylation-independent fashion in MDA-MB-231 and Tamoxifen-resistant MCF7 cells. Data from TCGA and GEO databases allowed us to explore the clinical implications of our results. An inverse correlation between CTCF and IL6 expression levels was seen in disease-free survival BrCa patients but not in patients who experienced cancer recurrence. Conclusions: Our findings provide evidence that the CTCF-mediated negative regulation of the IL6 gene is lost in highly tumorigenic BrCa cells.

ADAMTSs are extracellular matrix metalloproteinases that mainly process extracellular matrix components and closely related tumorigenesis. ADAMTS-8 is an anti-angiogenic member of the family and is dysregulated in common cancers. The tumor suppressor function of the ADAMTS-8 has been demonstrated in colorectal cancer. Although ADAMTS-8 plays a critical role in tumor progression, transcriptional regulatory features haven't been studied yet.

The human ADAMTS-8 promoter was cloned into the pMetLuc Reporter vector. Basal promoter activity and the effect of the IL-6 on ADAMTS-8 promoter activity were determined by transient transfection assays in SW480 cells. QRT-PCR and Western blot analyses assessed the impact of IL-6 on ADAMTS-8 mRNA and protein expressions. Functional binding of the specific transcription factors to the ADAMTS-8 promoter region was evaluated by ChIP qPCR and EMSA.

Our results demonstrated that the ADAMTS-8 promoter includes multiple binding sites for transcription factors that could be activated in the inflammatory pathways. IL-6 stimulation increased ADAMTS-8 promoter activity, also mRNA, and protein expressions. Pathway inhibition studies showed that IL-6-mediated induction of ADAMTS-8 was achieved through p38/MAPK, NF-κB, PI3K, and SAPK/JNK pathways. STATs, Elk-1, and c-Jun functionally bind to the ADAMTS-8 promoter region.

It can be concluded that inflammation is a strong positive regulator of the ADAMTS-8 gene.

To date, no drugs are approved for BK polyomavirus (BKPyV) reactivation, a major cause of nephropathy after kidney transplantation. Recently, tumor necrosis factor-α (TNF-α) blockade has been proposed as a promising therapy, however, the effect of TNF-α on the clinically most common archetype (ww) BKPyV remained unclear. Assays in primary renal proximal tubule epithelial cells (RPTEC) allowed efficient replication only of BKPyV strains with rearranged (rr) non-coding control regions (NCCR), which may develop at later disease stages, but not of ww-BKPyV. Here, we optimized culture conditions allowing robust replication of patient-derived ww-BKPyV, while efficiently preserving their ww-NCCR. TNF-α promoted rr-BKPyV replication, while the TH1 cytokine IFN-γ suppressed it, also in the presence of TNF-α. Surprisingly, TNF-α alone was sufficient to suppress all ww-BKPyV strains tested. Comprehensive analysis using siRNAs, and chimeric or mutated BKPyV-strains revealed that the response to TNF-α depends on the NCCR type, and that the NF-κB p65 pathway but not the conserved NF-κB binding site is essential for the TNF-α-induced enhancement of rr-BKPyV replication. Our data suggest that in immunosuppressed patients with archetype-dominated infections, TNF-α blockade could interfere with natural TNF-α-mediated anti-BKPyviral control, and this could be detrimental when IFN-γ-driven TH1 responses are impaired. Ongoing inflammation, however, could lead to the selection of rearrangements responding to NCCR-activating pathways downstream of NF-κB p65 signaling, that may overcome the initial TNF-α-mediated suppression. Our findings also highlight the importance of using clinically relevant BKPyV isolates for drug testing and discovery, for which this new assay paves the way.

Patients with sickle cell disease (SCD) experience pain in their daily lives. Both the acute and chronic pain phenotypes of this disease exhibit high variability, making pain management a challenge. The underlying reasons for the phenotypic variability are poorly understood. Given the importance of serotonergic neurotransmission in pain signaling, we aimed to explore the role of variants in the 5-HT1A receptor gene (HTR1A) on pain variability in SCD. Four variants (rs6449693, rs878567, rs6294, and rs10042486) in HTR1A were genotyped in a cohort of 131 African Americans with SCD. Acute and chronic pain were measured by the acute care utilization and the McGill Pain Questionnaire, respectively. Association analyses were performed for three genetic models (additive, dominant, and recessive). Three variants (rs6449693, rs6294, and rs10042486) in HTR1A showed significant association with crisis pain in both the additive and dominant models. Although the G allele of rs6449693 and the C allele of rs10042486 associated with lower acute crisis pain, the T allele of rs6294 associated with increased acute crisis pain. Sex-stratified analyses revealed that the associations of these three variants with acute pain were significant only in men, but not in women. Furthermore, the A allele rs878567 that did not reach statistical significance in the overall cohort showed a significant association with lower crisis pain in men. To our knowledge, as the first study to explore the role of HTR1A variants in sickle cell pain, we identified that four variants across the gene are associated with acute crisis pain in SCD in a sex-stratified manner.

Circular (circ)RNAs have emerged as crucial contributors to cancer progression. Nonetheless, the expression regulation, biological functions, and underlying mechanisms of circRNAs in mediating hepatocellular carcinoma (HCC) progression remain insufficiently elucidated.

We identified circUCK2(2,3) through circRNA sequencing, RT-PCR, and Sanger sequencing. CircUCK2(2,3) levels were measured in two independent HCC cohorts using quantitative real-time PCR (qRT-PCR). We explored the functions of circUCK2(2,3) using gain- and loss-of-function assays. Techniques such as RNA-sequencing, RNA immunoprecipitation (RIP), polysome fractionation, RNA pulldown, dual luciferase reporter assay, inhibitors of EGFR downstream signaling, CRISPR-Cas9, and medium transfer assays were employed to investigate the regulatory mechanisms and the protumoral activities of circUCK2(2,3). Additionally, in vitro cytotoxic assays and patient-derived xenograft (PDX) models assessed the effects of circUCK2(2,3) on the cytotoxic synergy of lenvatinib and EGFR inhibitors.

CircUCK2(2,3) is upregulated in HCC tissues and serves as an independent risk factor for poor recurrence-free survival. The expression of circUCK2(2,3) is independent on its host gene, UCK2, but is regulated by its upstream promoter and flanking inverted complementary sequences. Functionally, circUCK2(2,3) enhances HCC proliferation, migration, and invasion, both in vitro and in vivo. Mechanistically, by sponging miR-149-5p, circUCK2(2,3) increases CNIH4 levels, which in turn amplifies TGFα secretion, resulting in the activation of EGFR and downstream pAKT and pERK signaling pathways. Moreover, circUCK2(2,3) overexpression sensitizes HCC cells to EGFR inhibitors, and increases the synergistic cytotoxicity of combined lenvatinib and EGFR inhibitor treatment.

CircUCK2(2,3) regulates a novel oncogenic pathway, miR-149-5p-CNIH4-TGFα-EGFR, in HCC, presenting a viable therapeutic target and biomarker for the precision treatment of HCC.

Hearing loss is a prevalent condition with a significant impact on individuals' quality of life. However, comprehensive studies investigating the differential gene expression and regulatory mechanisms associated with hearing loss are lacking, particularly in the context of diverse patient samples. In this study, we integrated data from 10 patients across different regions, age groups, and genders, with their data retrieved from a public transcriptome database, to explore the molecular basis of hearing loss. These samples are mainly from fibroblasts and keratinocytes. Through differential gene expression analysis, we identified key genes, including ICAM1, SLC1A1, and CD24, which have already been shown to play important roles in neurogenic hearing loss. Furthermore, we predicted potential transcriptional regulatory factors that may modulate the expression of these genes. Enrichment analysis revealed biological processes and pathways associated with hearing loss, highlighting the involvement of circadian rhythm disruption and other neuro-related disorders. Although our study is limited by the sample size and the absence of larger-scale investigations, the identified genes and regulatory factors provide valuable insights into the molecular mechanisms underlying hearing loss. Further molecular and cellular experiments are necessary to validate these findings and elucidate the precise regulatory mechanisms involved. In conclusion, our study contributes to the understanding of hearing loss pathogenesis and offers potential targets for molecular diagnostics and gene-based therapies. This provides a foundation for further research into personalized approaches to diagnosing and treating hearing loss.

In our previous genome-wide association study on milk production traits in Chinese Holstein cows, HSF1 (heat shock factor 1) and CPSF1 (cleavage and polyadenylation specific factor 1) were found to be strongly associated with milk fat and protein percentages. However, their roles in milk fat and protein synthesis and the underlying mechanism are still largely unknown. In this study, we verified the effects of their expressions on milk fat and milk protein synthesis in MAC-T cells. We showed that HSF1 can participate in the AKT/mTOR signaling pathway, one of the most important pathways for fat and protein synthesis, through its interaction with the AKT protein and influence the downstream genes in this pathway to regulate milk fat and milk protein synthesis. We also found that HSF1, as a transcription factor, can bind to the promoter region of CPSF1 to regulate its transcription and expression, which in turn modulates the expression of SREBP1 and thereby influences the synthesis of milk fat.

Cervical cancer remains a significant global health concern. KIF18A, a kinesin motor protein regulating microtubule dynamics during mitosis, is frequently overexpressed in various cancers, but its regulatory mechanisms are poorly understood. This study investigates KIF18A's role in cervical cancer and its regulation by the JNK1/c-Jun signaling pathway. Cell growth was assessed in vitro using MTT and colony formation assays, and in vivo using a nude mouse xenograft model with KIF18A knockdown HeLa cells. The Genomic Data Commons (GDC) data portal was used to identify KIF18A-related protein kinases in cervical cancer. Western blot analysis was employed to analyze phosphor-c-Jun, c-Jun, and KIF18A expression levels following JNK1 inhibition, c-Jun knockdown/overexpression, and KIF18A knockdown in cervical cancer cells. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were performed to assess c-Jun binding and transcriptional activity of the KIF18A promoter. KIF18A knockdown significantly impaired cervical cancer cell growth both in vitro and in vivo. A strong positive correlation was observed between JNK1 and KIF18A expression in cervical and other cancers. JNK1 inhibition decreased both KIF18A expression and c-Jun phosphorylation. c-Jun was found to directly bind to and activate the KIF18A promoter. Furthermore, c-Jun knockdown inhibited cervical cancer cell growth, and this effect was partially rescued by KIF18A overexpression. This study demonstrates that the JNK1/c-Jun pathway activates KIF18A expression, which is essential for cervical cancer cell growth. Targeting the JNK/c-Jun/KIF18A axis may represent a promising novel therapeutic strategy for cancer treatment.

Cell division cycle-associated (CDCA) genes are dysregulated in carcinomas. Our study aims to identify similarities and differences of the clinical roles of CDCAs in breast cancer (BRCA) and to explore their potential mechanisms. In GEPIA, compared to normal tissues, expressions of CDCAs were higher in BRCA and sub-types. In addition, CDCAs were significantly positively related to stages and predicted worse survival in BRCA. In CancerSEA, expression levels of most CDCAs were strongly positively related to cell cycle, DNA damage, DNA repair, and proliferation. In TIMER, CDCAs were linked with immune infiltration levels of BRCA, including Dendritic cell, B cell and so on, and were positively related to most of the common markers of immune cells, especially CD38 of B cell and IL12RB2 of Th1. In GeneMANIA, there were complex interactions and co-expression relationships between CDCAs and cell division-associated genes. In addition, CDCA1, CDCA3, CDCA5, CDCA6 and CDCA8 had a high proportion of amplification in BRCA, and CDCA1, CDCA2, CDCA5, CDCA7 and CDCA8 had high levels of body DNA methylation. Among 11 transcription factors possibly combining promoters of all CDCAs, FOXP3 and YY1 were significantly higher in BRCA in comparison to normal tissues, and both had a positive relationship with all CDCAs in GEPIA and IHC. In addition, silencing FOXP3 or YY1 decreased levels of CDCAs in MDA-MB-231. In summary, CDCAs have various similarities in clinical functions, functional states, immune infiltration, and mechanisms, and they may become novel potential biomarkers for BRCA.

Decoy receptor 3 (DcR3), a soluble receptor in the tumor necrosis factor receptor superfamily, regulates the functions of monocytes, macrophages, dendritic cells, and T cells. Previous studies have demonstrated that DcR3 suppresses B cell proliferation in vitro and ameliorates autoimmune diseases in animal models; however, whether and how DcR3 regulates antibody production is unclear. Using a DcR3 transgenic mouse model, we found that DcR3 impaired the T cell-dependent antigen-stimulated antibody response. The number of Ag-specific antibody-secreting cells was transiently reduced, but the concentration of specific antibodies continued to decrease in the DcR3 transgenic mice, implying a direct suppression of antibody production by DcR3. In vitro assays showed that the DcR3-Fc fusion protein attenuated T cell-dependent induced antibody production and reduced the expression of secretory Igh and Xbp1. We found that nuclear factor κB (NF-κB) activity was essential for the expression of Xbp1 in activated B cells. DcR3-Fc attenuated anti-CD40-induced NF-κB activity and Xbp1 promoter activity. Furthermore, DcR3-Fc decreased the expression of Xbp1 in Blimp1+ antibody-secreting cells. Restoration of spliced XBP1 (X-box binding protein 1) in DcR3-treated B cells increased the secretory Ighg1 transcript levels, suggesting that reducing XBP1 is one of the mechanisms by which DcR3 regulates antibody production both in vitro and in vivo. Collectively, these results indicate that in addition to blocking proliferation, DcR3 impairs NF-κB activation, subsequently decreasing the expression of Xbp1, eventually leading to a reduction in antibody secretion.

Recently, the O-6-methylguanine-DNA methyltransferase (MGMT) locus was proposed as influencing the risk of Alzheimer's disease (AD) in women who did not carry the apolipoprotein E ε4 allele. We examined an Amish founder population for any influence of genetic variation in and around the MGMT locus on the risk for dementia.

Genetic association was performed for single nucleotide polymorphisms (SNPs) surrounding the MGMT locus. A total of 946 individuals of Amish descent between the ages of 76 and 95 who were classified as cognitively impaired or cognitively unimpaired were included. Multiple statistical models were applied to test for replication.

The results for the previously associated individual SNPs were not significant. However, a different SNP (rs7909468) generated significant results under a model different from the previous report.

The MGMT locus may influence the risk of AD, although its genetic mechanisms remain unclear and warrant further study.

Association analyses around the O-6-methylguanine-DNA methyltransferase (MGMT) locus showed a study-significant single nucleotide polymorphism (SNP), rs7909468, in a female cognitively impaired group lacking the apolipoprotein E ε4 genotype. Functional implications of rs7909468 are relatively unexplored, but in silico analyses indicate it may regulate MGMT expression. rs7909468 was not in linkage disequilibrium with other SNPs found to be significant in this region and appears as a distinct novel association.

Previous data show that the knockdown of the MYBL1 gene in the MDA-MB-231 cell line leads to the downregulation of VCPIP1 gene expression. In addition, MYBL1 and VCPIP1 genes are co-expressed and dysregulated in some of the same triple negative breast cancer patient samples. We propose that the co-expression of the two genes is attributed to the MYBL1 transcription factor regulation of the VCPIP1 gene. We identify the MYBL1 transcription factor binding site upstream of the VCPIP1 start site and show that the MYBL1 protein can bind to the sequence identified in the VCPIP1 promoter region. Combined with the results from the knockdown study, these data support the ability of MYBL1 to regulate the VCPIP1 gene. The VCPIP1 gene functions as a deubiquitinating enzyme involved in DNA repair, protein positioning, and the assembly of the Golgi apparatus during mitotic signaling. The transcriptional regulation of VCPIP1 by the MYBL1 gene could implicate MYBL1 in these processes, which might contribute to tumor processes in TNBC. Although both genes are involved in cell cycle regulatory mechanisms, converging signaling mechanisms have not been identified. In a separate study, we performed sequence alignment of the MYBL1 transcript variants and identified an exon unique to the canonical variant. Probes that specifically target the unique MYBL1 exon show that the exon is overexpressed in tumor cell lines compared to non-tumor breast cells. We are classifying this unique MYBL1 exon as a tumor-associated exon.

Hepatocellular carcinoma (HCC) is a lethal malignancy characterized by rapid growth. The interaction between tumor cells and cancer-associated fibroblasts (CAFs) significantly influences HCC progression. CCL15, a CC chemokine family member, is predominantly expressed in HCC and strongly correlates with tumor size, indicating its critical role in HCC growth. However, previous studies suggest that CCL15 does not directly stimulate cancer cell proliferation. The specific role and mechanism of CCL15 in HCC proliferation remain unknown. Here, we identified that CCL15 was predominantly overexpressed by HCC cells through single-cell RNA sequencing data and immunofluorescence. We discovered that CCL15 promotes HCC growth by stimulating the crosstalk between HCC cells and CAFs via CCR1 signaling, as evidenced by co-culture assays, organoid models, and allograft models. Mechanistically, CCL15 induced the expression of FTO in CAFs through the STAT3 pathway. By m6A sequencing and RNA sequencing, we found that CEBPA mRNA, a transcription factor regulating CXCL5 expression, was a target of FTO. CXCL5, secreted by CAFs, activated the CXCR2 receptor on HCC cells and enhanced their proliferation. Notably, we found that interfering with CCL15 signaling using a neutralizing antibody attenuated HCC growth in heterotypic co-injection and patient-derived xenograft murine models. Finally, CXCL5 also upregulated CCL15 expression in HCC cells by modulating P53 expression through MDM2, forming a positive feedback loop. Our study unveiled CCL15 as a key mediator in HCC progression, facilitating communication between HCC cells and CAFs. This highlights a novel regulatory axis in HCC and suggests that targeting CCL15 could be a potential therapeutic strategy.

Non-classical MHC class I genes which, compared to classical MHC class I, are typically less polymorphic and have more restricted expression patterns are attracting interest because of their potential to regulate immune responses to various pathogens. In salmonids, among the numerous non-classical MHC class I genes identified to date, L lineage genes, including Sasa-LIA and Sasa-LGA1, are differentially induced in response to microbial challenges. In the present study, we show that while transcription of both Sasa-LIA and Sasa-LGA1 are induced in response to SAV3 infection the transcriptional induction patterns are distinct for each gene. While elevated Sasa-LGA1 expression is maintained long-term following in vivo SAV3 infection Sasa-LIA expression is transient, returning to near baseline weeks prior to viral clearance. Furthermore, by contrasting L lineage transcriptional induction potential of SAV3 with that of IPNV we show that Sasa-LIA and Sasa-LGA1 transcriptional induction is tightly interconnected with select type I and type II interferon induction. Both type I and type II interferon stimulation, to varying degrees, induce Sasa-LIA and Sasa-LGA1 expression. Compared to IFNa1 and IFNc, IFN-gamma was a more effective inducer of both Sasa-LIA and Sasa-LGA1 while IFNb showed no activity. Furthermore, IFNa was a more potent inducer of Sasa-LIA compared to IFNc. The involvement of type I IFN and IFN gamma in regulation of Sasa-LIA and Sasa-LGA1 expression was further substantiated by analysis of their respective promoter regions which indicate that ISRE and GAS like elements most likely cooperatively regulate Sasa-LIA expression while IFN gamma induced expression of Sasa-LGA1 is critically dependent on a single, proximally located ISRE element. Together, these findings imply that Sasa-LIA and Sasa-LGA1 play important but likely functionally distinct roles in the anti-viral response of salmonids and that these two molecules may serve as immune regulators promoting more effective antiviral states.

Chronic infection with hepatitis B virus (HBV) remains an important public health challenge. Viral covalently closed circular DNA (cccDNA) persists in infected hepatocytes and serves as the template for transcribing all viral RNA species. HBV regulatory protein X (HBx) interacts with other viral and cellular proteins to play diverse functions in viral life cycle, including modulation of cccDNA transcription activity. Here, we used proximity labeling coupled with proteomic analysis to screen for HBx-interacting host proteins. One of the identified candidates, deubiquitinating enzyme valosin-containing protein-interacting protein 1 (VCPIP1), directly binds HBx and stabilizes HBx by reducing its proteasomal degradation, which corroborated a recent report. VCPIP1-mediated upregulation of HBV transcription, antigen expression, and genome replication was demonstrated using a series of HBV replication and infection models. More importantly, VCPIP1 was found to upregulate HBV in the absence of HBx. Mechanistic studies revealed that VCPIP1 HBx-independently associates with HBV enhancer I/X promoter (EnI/Xp) and positively modulates both its promoter and enhancer activities, partially through promoting the binding of YY1 transcription factor to EnI/Xp. Results presented here expand the recently described role of VCPIP1 in HBV life cycle and establish it as a multi-functional positive regulator of this virus.

Hepatitis B virus (HBV) encodes the regulatory protein HBx that plays crucial roles in viral life cycle and cellular processes through interacting with viral and cellular proteins. Identifying HBx-interacting proteins may reveal novel aspects of host-virus interactions. In this work, proximity labeling coupled with proteomic analysis identified multiple HBx-interacting host factors, and among these, valosin-containing protein-interacting protein 1 (VCPIP1) was confirmed to directly bind HBx and reduce its proteasomal degradation, corroborating a recent report. In addition to upregulating HBx-expressing HBV, we showed that VCPIP1 also positively regulates mutant HBV lacking HBx expression. This novel HBx-independent function of VCPIP1 was shown to involve its association with one viral promoter/enhancer element, which upregulated the latter's promoter and enhancer activities. These results establish VCPIP1 as a positive regulator of HBV that acts through multiple, diverse mechanisms and might also contribute toward revealing novel cellular functions of VCPIP1.